Prepare Ubuntu 24.04 for Spatial Ecology courses

In order to execute the Spatial Ecology exercise we will need first install the Ubuntu 24.04 Linux Virtual Machine and then populate with additional software and data.

Ubuntu 24.04 Noble Numbat is a Linux Virtual Machine, that allows you to try a wide variety of open source geospatial software previous installation anything. It is composed entirely of free software, allowing it to be freely distributed, duplicated and passed around.

You can follow the below instructions. Moreover the Ubuntu 24.04 LTS installation YouTube video even if use another VM image can be used to guide along the full procedure. Pay attention that the video is base on the Osgeolive 13 version, so some differences can be present comparing with the current Ubuntu 24.04 version.

Software requirements

For running a Virtual Machine in your OS we need a virtualization software such as Virtualbox and a vmdk or vdi file that contains the virtualized OS.

Hardware requirements

Hard disk

Be sure to have at least 60 GIGA of free space in your hard disk before to start the VM installation procedure. Avoid the use of USB-external-hard-disk, due that the USB connection will slow down the VM performance.

RAM

Be sure that your computer have at lest 16 GIGA ram (more better). Indeed with the VM running and the zoom session open for following the lecture the 16 GIGA will be barely on the limit.

Install Virtualbox

Open you browser and go to https://www.virtualbox.org/wiki/Downloads and base on your OS download the Virtualbox executable and install it. Be sure you also install the VirtualBox 7.2.0 Extension Pack.

Install Ubuntu 24.04 LTS Noble Numbat

Download Ubuntu 24.04

Open you browser and go to https://www.osboxes.org and proceed to download the Ubuntu 24.04 Noble Numbat for VirtualBox. This action will download the 64bit.7z file. The 64bit.7z is a quite large file therefore according to your Internet connection it can take several hours. When the download is finished unzipped using 7zip. Mac users can use The Unarchiver for unzip the 64bit.7z. A this point you are ready to load the Ubuntu 24.04 (64bit).vdi inside Virtualbox.

Install Ubuntu 24.04 inside Virtualbox

Lunch Virtualbox from OS and follow the below instructions.

Test your Ubuntu 24.04 LTS Virtual Machine

If you follow all the steps correctly the Ubuntu 24.04 LTS Virtual Machine should pop-up in the Virtual Box window showing something like this:

If the Ubuntu 24.04 LTS start with a black screen with a “kernel panic message” means that there are still some settings that are not allowing the virtualization. This page is a good tutorial for solving the issues in Windows-10 and this one for Windows-11.

Setting you keyboard layout

If are not use the US keyboard you have to add your keyboard layout to the bottom menubar. Therefore click on the spiral on the left bottom corner and write “keyboard” in the search box, and select in settings Keyboard.

Then select “Add Input Source” > “Add” and select your keyboard layout in accordance to your country and language.

Your keyboard layout will appear as below. Move up to select it as default keyboard layout.

Open the terminal and test if the keyboard layout is correct.

Update the OS

The first operation after the installation is to run un update of the OS. Therefore, open the bash terminal and run line by line the following codes. The sudo password is “osboxes.org”. For security what you type is not shown, anyway it is recorded. After typed the password press enter.

Update the OS. This operation can last few minutes. Be patient. If during the installation, some screen pop-up asking some question just accept the default option.

sudo apt update      # update the repositories
sudo apt upgrade -y  # installation of the sw
sudo apt autoremove -y

Test your shared folder

Another test that you should do, is to see if the shared folder is correctly done. Open a bash terminal and run

ls /media/sf_LVM_shared

If are able to list the folder then means that the sharing folder operation is properly done. Moreover try to insert a file from your host OS in the LVM_shared folder and see if visible in the Ubuntu 24.04 LTS.

If you get an error “ls: cannot access ‘/media/sf_LVM_shared’: No such file or directory” means that you did not correctly done the sharing folder operation or the Virtual Box Guest Additions installation, thus try to redo it.

If you get permission denied in accessing ‘/media/sf_LVM_shared’ run this commands

sudo usermod -a -G vboxsf osboxes
sudo chown -R osboxes:osboxes /media/sf_LVM_shared

You will need to reboot to make the folder accessible.

Populate Ubuntu 24.04 LTS with additional software

Install geo-software

At this point the Ubuntu 24.04 LTS Virtual Machine is ready to install additional software and data for running Spatial Ecology courses. In the bash terminal run the following lines

cd /tmp/
wget https://raw.githubusercontent.com/selvaje/SE_data/refs/heads/master/exercise/install_additional_sw_data_4SE_courses.sh 
sudo bash ./install_additional_sw_data_4SE_courses.sh

as before the sudo password is osboxes.org.

If a prompt asks for user input, just use the arrow keys to select the default option and press Enter.

Test installed additional software

In the bash terminal run the following lines one by one. Close the window that each time pop-up.

Test gdal

gdal_translate --version 

You should see the gdal version GDAL 3.8.4, released 2024/02/08

Test pktools

pkfilter --help

You should see the pkfilter manual instructions.

Test OpenEV

source ~/.bashrc
openev

You should see the openev software popup.

Git Settings

The below instructions together with the Git Setting for the Spatial Ecology courses YouTube video can guide along the full procedure to retrieve dataset and material for the courses.

We are going to retrieve dataset and material for the first time using git clone.

cd                                 # enter in user home
git clone https://github.com/selvaje/SE_data  # download the data 

If the download succeed you should see the SE_data folder

ls -l $HOME/SE_data 

Now we need copy the $HOME/SE_data to an independent directory the:
/media/sf_\LVM_shared/my_SE_data

rsync -hvrPt --ignore-existing ~/SE_data/* /media/sf_LVM_shared/my_SE_data
cd /media/sf_LVM_shared/my_SE_data

The /media/sf_LVM_shared/my_SE_data is your working directory. Do not touch the ~/SE_data folder!!

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Every time that we need to download more data from the git repository, follow this procedure

cd $HOME/SE_data
git pull
rsync -hvrPt --ignore-existing $HOME/SE_data/* /media/sf_LVM_shared/my_SE_data
cd /media/sf_LVM_shared/my_SE_data

Now you should be ready to follow the lectures of the Spatial Ecology courses.
Remember always to work on /media/sf_LVM_shared/my_SE_data

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If for any reason the git pull commands give a synchronized error you need to remove the $HOME/SE_data and repeat the git clone and rsync operation.

cd
rm -ry $HOME/SE_data
git clone https://github.com/selvaje/SE_data
rsync -hvrPt --ignore-existing $HOME/SE_data/* /media/sf_LVM_shared/my_SE_data
cd /media/sf_LVM_shared/my_SE_data

Install jupyter lab

We are going to use jupyter lab as main scripting editor. Here how to install

sudo apt install pipx
pipx ensurepath
pipx install jupyterlab
echo 'export PATH=$PATH:$HOME/.local/bin' >> ~/.bashrc
source ~/.bashrc

Test jupyter lab

jupyter-lab /media/sf_LVM_shared/my_SE_data/exercise/grass_hydro.ipynb

Get familiar with the jupyter lab GUI.